When Metchnikoff discovered phagocytosis, he speculated that macrophages kill most ingested microbes by acidifying them and that Mycobacterium tuberculosis (“Mtb”) uses its waxy cell wall to resist this acidification (Metchnikoff, “Immunity to Infective Disease,” Cambridge University Press; Cambridge, London, N.Y. (1905)). Subsequent studies established that after macrophages ingest particles or microbes, phagosomes with an initial pH of ˜6.2 fuse with lysosomes, and their pH falls to ˜4.5 (Huynh et al., “Regulation of Vacuolar pH and its Modulation by Some Microbial Species,” Microbiol Mol Biol Rev 71:452-462 (2007) and Ohkuma et al., “Fluorescence Probe Measurement of the Intralysosomal pH in Living Cells and the Perturbation of pH by Various Agents,” Proc Natl Acad Sci USA 75:3327-3331 (1978)). Mtb blocks phagolysosomal fusion (Armstrong et al., “Response of Cultured Macrophages to Mycobacterium Tuberculosis, with Observations on Fusion of Lysosomes with Phagosomes,”J Exp Med 134:713-740 (1971); Sturgill-Koszycki et al., “Lack of Acidification in Mycobacterium Phagosomes Produced by Exclusion of the Vesicular Proton-ATPase,” Science 263:678-681 (1994); and Clemens et al., “Characterization of the Mycobacterium Tuberculosis Phagosome and Evidence that Phagosomal Maturation is Inhibited,” J Exp Med 181:257-270 (1995)); however, activation of macrophages by the T cell-derived cytokine IFN-γ overcomes the block via induction of the GTPase Lrg-47, and thus the mycobacterium-containing phagosomes acidify (MacMicking et al., “Immune Control of Tuberculosis by IFN-γ-Inducible LRG-47,” Science 302:654-659 (2003); Schaible et al., “Cytokine Activation Leads to Acidification and Increases Maturation of Mycobacterium Avium-Containing Phagosomes in Murine Macrophages,” J Immunol 160:1290-1296 (1998); Via et al., “Effects of Cytokines on Mycobacterial Phagosome Maturation,” J Cell Sci 111:897-905 (1998); and Sibley et al., “Intracellular Fate of Mycobacterium Leprae in Normal and Activated Mouse Macrophages,” Infect Immun 55:680-685 (1987). Additionally, IFN-γ activation enhances the antimicrobial capacity of macrophages (Nathan et al., “Identification of Interferon-γ as the Lymphokine that Activates Human Macrophage Oxidative Metabolism and Antimicrobial Activity,” J Exp Med 158:670-689 (1983)) and is essential for control of mycobacterial infection in mice and people (Nathan et al., “Local and Systemic Effects of Intradermal Recombinant Interferon-γ in Patients with Lepromatous Leprosy,” N Engl J Med; 315:6-15 (1986); Cooper et al., “Disseminated Tuberculosis in Interferon-γ Gene-Disrupted Mice,” J Exp Med 178:2243-2247 (1993); Flynn et al., “An Essential Role for Interferon-γ in Resistance to Mycobacterium Tuberculosis Infection,” J Exp Med 178:2249-2254 (1993); and Dorman et al., “Clinical Features of Dominant and Recessive Interferon-γ Receptor 1 Deficiencies,” Lancet 364:2113-2121 (2004)). Thus, acidification of the phagosome may represent a major antimycobacterial mechanism. However, IFN-γ induces hundreds of genes in macrophages (Ehrt et al., “Reprogramming of the Macrophage Transcriptome in Response to Interferon-γ and Mycobacterium Tuberculosis: Signaling Roles of Nitric Oxide Synthase-2 and Phagocyte Oxidase,” J Exp Med 194:1123-1140 (2001)), among them other pathways with antimycobacterial activity, such as inducible nitric oxide synthase (Xie et al., “Cloning and Characterization of Inducible Nitric Oxide Synthase from Mouse Macrophages,” Science 256:225-228 (1992) and MacMicking et al., “Identification of Nitric Oxide Synthase as a Protective Locus Against Tuberculosis,” Proc Natl Acad Sci USA 94:5243-5248 (1997)). Because Mtb is killed to an extent, but not eradicated, in acidic phagosomes, it is unclear whether Mtb should be regarded as acid sensitive or acid resistant (Armstrong et al., “Phagosome-Lysosome Interactions in Cultured Macrophages Infected with Virulent Tubercle Bacilli. Reversal of the Usual Nonfusion Pattern and Observations on Bacterial Survival,” J Exp Med 142:1-16 (1975); MacGurn et al., “A Genetic Screen for Mycobacterium Tuberculosis Mutants Defective for Phagosome Maturation Arrest Identifies Components of the ESX-1 Secretion System,” Infect Immun 75:2668-2678 (2007)). In addition, mutants of Mtb and Mycobacterium bovis BCG that fail to prevent phagosome acidification are not necessarily compromised for survival in macrophages, suggesting that the bacterium can resist acid (MacGurn et al., “A Genetic Screen for Mycobacterium Tuberculosis Mutants Defective for Phagosome Maturation Arrest Identifies Components of the ESX-1 Secretion System,” Infect Immun 75:2668-2678 (2007); Pethe et al., “Isolation of Mycobacterium Tuberculosis Mutants Defective in the Arrest of Phagosome Maturation,” Proc Natl Acad Sci USA 101:13642-13647 (2004); and Stewart et al., “Mycobacterial Mutants with Defective Control of Phagosomal Acidification,” PLoS Pathog 1:269-278 (2005)).
There is a continuing need to develop new anti-tuberculosis agents, especially those having unique modes of action, to ensure the availability of effective treatments against multi- and extreme-drug resistant strains. Therefore, a better understanding of M. tuberculosis acid resistance or sensitivity and its role in virulence is necessary. Such information will aid the development of new antibiotic agents that will complement conventional anti-tuberculosis chemotherapeutic regimens. The present invention is directed to overcoming these and other deficiencies in the art.